v1.7.0

Changed

• VCFs generated by the --sv option are now automatically annotated with SnpEff, incorporating ClinVar annotations
  • This can be switched off with --skip_annotation
• —-skip_annotation disables attempt to determine human genome version, enabling --snp, --sv and --phase_methyl to be called on genomes which aren’t hg19 or hg38
• Updated example command displayed when running --help
• The ClinVar table in --snp and --sv reports is now sorted according to clinical significance, and includes HGVS cDNA and protein descriptions
• Workflow options for disabling steps have been updated for consistency:
  • --skip_annotation is now --annotation false
  • --skip_refine_snp_with_sv is now --refine_snp_with_sv false
• --phase_methyl also calls modifications using all reads to account for unphased regions
• Input options and Output options have been combined in the Main options category
• Updated Clair3 to v1.0.4
• SV workflow does not filter the SV calls by size and type
• Report for bam files failing the depth threshold is now consistent with the report of bam passing the hard threshold
• Perform Sniffles SV phasing with --phase_sv
• --phase_vcf now run Sniffles SV in phasing mode

Fixed

• 'mosdepth_downsampled' is defined more than once warning
• Workflow crashing when providing a reference with spaces/brackets in file name
• Workflow not emitting GVCF even when requested
• GVCF sample name not matching sample_name
• --cnv subworkflow sometimes reporting incorrect genetic sex, due to the way segment copy numbers were aggregated across chromosomes

Added

• Add downsampling of large bam files
• --joint_phasing allows an additional joint SNP and SV phasing
• --joint_phasing and --phase_vcf now emit a phased block GTF file to facilitate visualization

Removed

• --sv_types, all SV types are returned without filtering
• --max_sv_length, all SVs are returned regardless of maximum size